Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019522.1 Corchorus olitorius cultivar O-4 contig19555, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3852
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:1068 original size:334 final size:328
Alignment explanation
Indices: 221--1072 Score: 1049
Period size: 334 Copynumber: 2.6 Consensus size: 328
211 ATTCATATGC
* *
221 GTTAGATGGATATAGATATTTCAATGAGACTTGGTGCCAAAAATTGTGCAAAACTGAGCCGGGGC
1 GTTAGATGGATATAGATATTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACTGAGCCGGGGC
*
286 TCTAGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAA
66 TCCAGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAA
* *
351 AAATTGACCCGAGAAAATTTCTCCTCAATTTCCGGCCACCATATTCATAAAAAA-ATATATAATT
131 AAATTGACCCG-GAAAATTTCTCCTCAATTT-CGGCCACAATACTCATAAAAAATATATATAATT
* *
415 CAACGCCAAAAGATAGAAGGACTTTCACGCTTCCAATTTTTTTCTATTTTTTCCGAATTAATTTG
194 CAACACCAAAAGATAGAAGGACTTTCACGCTTCCAATTTTTTTCTATTTTTACCGAATTAATTTG
* * * *
480 TAATTAAATCGATATCGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGA
259 CAATTAAATCGATAACGGATTCAGATGCTCGTAAAAACAAATCCTTAAATACAATGTGGCTAAGA
545 ATTAT
324 ATTAT
* * * * * * *
550 -TTAGATGAATATAGATATTTCAATGAGTCTTGGC-ACAAAAATCATACAAAACTAAGCCGGAGC
1 GTTAGATGGATATAGATATTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACTGAGCCGGGGC
* * * * *
613 CCCGGAACGCGTTTTTAG-CAAAAAAAACCGTGATAGTTAGCACACGATTTCGGCTAAAATTTTG
66 TCCAGAACGCGTTTTTAGTC---AAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTG
* * * * * *
677 TAAAAATTGACCCGAAAGAATTT-TCCTCAATTTTTGGCCACAACACTCATAAAAAATATGTTTA
128 CAAAAATTGACCCGGAA-AATTTCTCCTCAA-TTTCGGCCACAATACTCATAAAAAATATATATA
* * * *
741 ATTCAACACCAAAAAGATTGAAATG-TTATTCACGCTTCTAATATAGTTTTTCCTATTTTTACCG
191 ATTCAACACC-AAAAGATAG-AAGGACT-TTCACGCTTCCAAT-T--TTTTT-CTATTTTTACCG
* * * **
805 AATTAATTCT-CAATTGAATCGA-AACATGATTCATATGCTCGTAAAAACAAATGTTTAAATACA
249 AATTAATT-TGCAATTAAATCGATAAC-GGATTCAGATGCTCGTAAAAACAAATCCTTAAATACA
* *
868 ATGTGGGTAAG-ATTTT
312 ATGTGGCTAAGAATTAT
*
884 GGTTAGATGGATATAGAT-TTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACTGAGTCGGGG
1 -GTTAGATGGATATAGATATTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACTGAGCCGGGG
* *
948 CTCCATAACGCGTTTTTAGTCTAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCA
65 CTCCAGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCA
* * * *
1013 AAAATTGACCCGGGAAATTTCTCCTCAATGTTGGGCCATAATACTAATAAAAAATATATA
130 AAAATTGACCCGGAAAATTTCTCCTCAAT-TTCGGCCACAATACTCATAAAAAATATATA
1073 ATTTTACGCC
Statistics
Matches: 438, Mismatches: 64, Indels: 37
0.81 0.12 0.07
Matches are distributed among these distances:
326 1 0.00
327 38 0.09
328 58 0.13
329 74 0.17
330 9 0.02
331 16 0.04
332 1 0.00
333 6 0.01
334 94 0.21
335 86 0.20
336 54 0.12
337 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (328 bp):
GTTAGATGGATATAGATATTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACTGAGCCGGGGC
TCCAGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAA
AAATTGACCCGGAAAATTTCTCCTCAATTTCGGCCACAATACTCATAAAAAATATATATAATTCA
ACACCAAAAGATAGAAGGACTTTCACGCTTCCAATTTTTTTCTATTTTTACCGAATTAATTTGCA
ATTAAATCGATAACGGATTCAGATGCTCGTAAAAACAAATCCTTAAATACAATGTGGCTAAGAAT
TAT
Done.